blackrim / phlawd_db_maker Goto Github PK

If one has a DB floating around for a while, or several DBs, it might be difficult to recall which version they represent. This pull request downloads the files README.genbank and GB_Release_Number. The latter file consists of only the version number.

Could this be added as a callable property of the DB? Might be useful.

I downloaded all the sequences for a clade and it provided a .gb file (also converted into a fasta). I don't have space to download the entire PLN division, but would really like to use pyphlawd.

And how does one go about doing it?

I have downloaded the pln database. The current version is 168 GB. However, this one seems to be corrupted. When I try to run the setup_clade.py command on it, I get an error.

I have tried to check if the file is corrupt. For this I did a rows count in the taxonomy table and I get a value of 0. However the rows count of the sequence table has a reasonable value. 3.5 million approximately.

Do you know of anyone who has had a similar problem?

I followed the instruction to use sqlitewrapper and copy it over but still get this:

[ 25%] Building CXX object CMakeFiles/phlawd_db_maker.dir/src/utils.cpp.o
/home/yayang/apps/phlawd_db_maker/src/utils.cpp:132:42: warning: unknown escape sequence: '.'
if(*(string(dirp->d_name).begin())=='.')
^
/home/yayang/apps/phlawd_db_maker/src/utils.cpp: In function ‘int getdir(std::string, std::vector<std::basic_string >&)’:
/home/yayang/apps/phlawd_db_maker/src/utils.cpp:123:29: error: ‘errno’ was not declared in this scope
cout << "Error(" << errno << ") opening " << dir << endl;
^
CMakeFiles/phlawd_db_maker.dir/build.make:123: recipe for target 'CMakeFiles/phlawd_db_maker.dir/src/utils.cpp.o' failed
make[2]: *** [CMakeFiles/phlawd_db_maker.dir/src/utils.cpp.o] Error 1
CMakeFiles/Makefile2:60: recipe for target 'CMakeFiles/phlawd_db_maker.dir/all' failed
make[1]: *** [CMakeFiles/phlawd_db_maker.dir/all] Error 2
Makefile:76: recipe for target 'all' failed
make: *** [all] Error 2

Some version issue perhaps?

when I tried to run "make", the error "Database.cpp:42:10: fatal error: sqlite3.h: No such file or directory" occurred. I learned that it may be due to the problem of sqlite3-dev, but I don't have the admin privileges. I can't use sudo apt-get to install it. Whether it is possible to place an already built database in the software folder (such as pln).

is there a specific reason this was done in C++? This stuff is more script than anything, so I'm surprised it wasn't done in python. Since it is in C++, however, it might be more efficient to use NCBI's E-utilities library to do the database downloading, or at least use http instead of ftp and parallelize it with openmp. some of the other slower parts could also probably be parallelized/vectorized with an OMP pragma or two.

Hi,

I tried to installed phlawd_db_maker on my own Mac following the instructions. It seems working all the way until the last step:

1 warning generated.
[100%] Linking CXX executable phlawd_db_maker
Undefined symbols for architecture x86_64:
"Query::get_result(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&)", referenced from:
SQLiteDBController::initiate() in SQLiteDBController.cpp.o
SQLiteDBController::load_seqs(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator >, bool) in SQLiteDBController.cpp.o
"Database::Database(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator > const&, IError*)", referenced from:
SQLiteDBController::initiate() in SQLiteDBController.cpp.o
SQLiteDBController::load_seqs(std::__1::basic_string<char, std::__1::char_traits, std::__1::allocator >, bool) in SQLiteDBController.cpp.o
"std::__cxx11::basic_string<char, std::char_traits, std::allocator >::_M_replace(unsigned long, unsigned long, char const*, unsigned long)", referenced from:
Query::get_string(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&) in libsqlitewrapped.a(Query.o)
"std::__cxx11::basic_string<char, std::char_traits, std::allocator >::reserve(unsigned long)", referenced from:
std::__cxx11::basic_string<char, std::char_traits, std::allocator > std::operator+<char, std::char_traits, std::allocator >(char const*, std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&) in libsqlitewrapped.a(Query.o)
"std::__cxx11::basic_string<char, std::char_traits, std::allocator >::_M_append(char const*, unsigned long)", referenced from:
std::__cxx11::basic_string<char, std::char_traits, std::allocator > std::operator+<char, std::char_traits, std::allocator >(char const*, std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&) in libsqlitewrapped.a(Query.o)
Database::xmlsafestr(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&) in libsqlitewrapped.a(Database.o)
"std::__cxx11::basic_string<char, std::char_traits, std::allocator >::_M_assign(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&)", referenced from:
Query::execute(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&) in libsqlitewrapped.a(Query.o)
Query::get_result(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&) in libsqlitewrapped.a(Query.o)
"std::__cxx11::basic_string<char, std::char_traits, std::allocator >::_M_create(unsigned long&, unsigned long)", referenced from:
void std::__cxx11::basic_string<char, std::char_traits, std::allocator >::_M_construct<char const*>(char const*, char const*, std::forward_iterator_tag) (.isra.43) in libsqlitewrapped.a(Query.o)
void std::__cxx11::basic_string<char, std::char_traits, std::allocator >::_M_construct<char const*>(char const*, char const*, std::forward_iterator_tag) (.isra.40) in libsqlitewrapped.a(Database.o)
"std::__cxx11::basic_string<char, std::char_traits, std::allocator >::_M_mutate(unsigned long, unsigned long, char const*, unsigned long)", referenced from:
Database::safestr(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&) in libsqlitewrapped.a(Database.o)
Database::xmlsafestr(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&) in libsqlitewrapped.a(Database.o)
"std::__detail::_List_node_base::_M_hook(std::__detail::_List_node_base*)", referenced from:
Database::grabdb() in libsqlitewrapped.a(Database.o)
"std::__detail::_List_node_base::_M_unhook()", referenced from:
Database::~Database() in libsqlitewrapped.a(Database.o)
"std::_Rb_tree_decrement(std::_Rb_tree_node_base*)", referenced from:
std::_Rb_tree<std::__cxx11::basic_string<char, std::char_traits, std::allocator >, std::pair<std::__cxx11::basic_string<char, std::char_traits, std::allocator > const, int>, std::_Select1st<std::pair<std::__cxx11::basic_string<char, std::char_traits, std::allocator > const, int> >, std::less<std::__cxx11::basic_string<char, std::char_traits, std::allocator > >, std::allocator<std::pair<std::__cxx11::basic_string<char, std::char_traits, std::allocator > const, int> > >::_M_get_insert_unique_pos(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&) in libsqlitewrapped.a(Query.o)
std::_Rb_tree<std::__cxx11::basic_string<char, std::char_traits, std::allocator >, std::pair<std::__cxx11::basic_string<char, std::char_traits, std::allocator > const, int>, std::_Select1st<std::pair<std::__cxx11::basic_string<char, std::char_traits, std::allocator > const, int> >, std::less<std::__cxx11::basic_string<char, std::char_traits, std::allocator > >, std::allocator<std::pair<std::__cxx11::basic_string<char, std::char_traits, std::allocator > const, int> > >::_M_get_insert_hint_unique_pos(std::_Rb_tree_const_iterator<std::pair<std::__cxx11::basic_string<char, std::char_traits, std::allocator > const, int> >, std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&) in libsqlitewrapped.a(Query.o)
"std::_Rb_tree_increment(std::_Rb_tree_node_base*)", referenced from:
std::_Rb_tree<std::__cxx11::basic_string<char, std::char_traits, std::allocator >, std::pair<std::__cxx11::basic_string<char, std::char_traits, std::allocator > const, int>, std::_Select1st<std::pair<std::__cxx11::basic_string<char, std::char_traits, std::allocator > const, int> >, std::less<std::__cxx11::basic_string<char, std::char_traits, std::allocator > >, std::allocator<std::pair<std::__cxx11::basic_string<char, std::char_traits, std::allocator > const, int> > >::_M_get_insert_hint_unique_pos(std::_Rb_tree_const_iterator<std::pair<std::__cxx11::basic_string<char, std::char_traits, std::allocator > const, int> >, std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&) in libsqlitewrapped.a(Query.o)
"std::__throw_logic_error(char const*)", referenced from:
void std::__cxx11::basic_string<char, std::char_traits, std::allocator >::_M_construct<char const*>(char const*, char const*, std::forward_iterator_tag) (.isra.43) in libsqlitewrapped.a(Query.o)
void std::__cxx11::basic_string<char, std::char_traits, std::allocator >::_M_construct<char const*>(char const*, char const*, std::forward_iterator_tag) (.isra.40) in libsqlitewrapped.a(Database.o)
"std::__throw_length_error(char const*)", referenced from:
std::__cxx11::basic_string<char, std::char_traits, std::allocator > std::operator+<char, std::char_traits, std::allocator >(char const*, std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&) in libsqlitewrapped.a(Query.o)
Database::xmlsafestr(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&) in libsqlitewrapped.a(Database.o)
"std::_Rb_tree_rebalance_for_erase(std::_Rb_tree_node_base*, std::_Rb_tree_node_base&)", referenced from:
Query::free_result() in libsqlitewrapped.a(Query.o)
"std::_Rb_tree_insert_and_rebalance(bool, std::_Rb_tree_node_base*, std::_Rb_tree_node_base*, std::_Rb_tree_node_base&)", referenced from:
std::_Rb_tree<std::__cxx11::basic_string<char, std::char_traits, std::allocator >, std::pair<std::__cxx11::basic_string<char, std::char_traits, std::allocator > const, int>, std::_Select1st<std::pair<std::__cxx11::basic_string<char, std::char_traits, std::allocator > const, int> >, std::less<std::__cxx11::basic_string<char, std::char_traits, std::allocator > >, std::allocator<std::pair<std::__cxx11::basic_string<char, std::char_traits, std::allocator > const, int> > >::_M_insert_node(std::_Rb_tree_node_base*, std::_Rb_tree_node_base*, std::_Rb_tree_node<std::pair<std::__cxx11::basic_string<char, std::char_traits, std::allocator > const, int> >*) in libsqlitewrapped.a(Query.o)
ld: symbol(s) not found for architecture x86_64

clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[2]: *** [phlawd_db_maker] Error 1
make[1]: *** [CMakeFiles/phlawd_db_maker.dir/all] Error 2
make: *** [all] Error 2

Please help and let me know if you need more information. I have downloaded old pln database, however, I may also need to run the most updated database.

Thanks!

Miao

Dear professor,

Files of gbvtr.seq.gz were downloaded by ./phlawd_db_maker vrt ~/Desktop/vtr.db:

There was an error when I tried to unzip:

So...

Best regard,
Ran

Hi,

When I tried "cmake . ", an error was as followed: "does not appear to contain CMakeLists.txt", but it was there.

I used ubuntu in windows.

Kind regard,
Ran